Deo, D. | bioRxiv Science

bioRxiv2022

Novel and simple simulation method to design and development of antisense template

Antisense technology is emerging as potential therapeutics against lethal infections. Basically, Antisense-mRNA complex inhibits the protein translation of pathogens and thus it is used for treatment. Based on previous online tools and literatures and difficulties for designing antisense template, finding high conserved regions from large number of long sequences, by taking all those factors in consideration, we proposed new innovative offline target simulation methods i.e. Deletion of unwanted region from viral sequence alignment (DURVA) and Most frequent region (MFR) for designing and developing antisense template from large number of long sequence or genomic data. Based on current pandemic crisis and long genomic sequence of SARS-CoV-2, we chose coronavirus for simulation. Initially, we hypothesized that DURVA-MFR would find stable region from large annotated sequencing data. As per Chan et.al. guidelines for antisense designing and development, we designed couple of algorithms and python scripts to process the data of approximately 30kbp sequence length and 1Gb file size in short turnaround time. The steps involved were as: 1) Simplifying whole genome sequence in single line; 2) Deletion of unwanted region from Virus sequence alignment(DURVA); 3)Most frequent antisense target region(MFR) and 4)Designing and development of antisense template. This simulation method is identifying most frequent regions between 20-30bp long, GC count[≥]10. Our study concluded that targets were highly identical with large population and similar with high number of remaining sequences. In addition, designed antisense sequences were stable and each sequence is having tighter binding with targets. After studying each parameter, here we suggested that our proposed method would be helpful for finding best antisense against all present and upcoming lethal infection.The initial design of this logic was published in Indian Patent Office Journal No.08/2021withApplication number202121005964A. Simple summaryThe antisense development is state of the art for modern therapeutics. There are number of online soft-wares and open sources for designing of antisense template. But all other tools did not consider frequency as major factor for designing antisense. Also; all sources excepting our simulation approach does not process large file or long sequences. Therefore; we designed an offline innovative simulation method which deletes the unwanted region from sequences and stores the data which are fulfilled antisense criteria. Further; the calculation of frequency from these short listed target regions; the most frequent region is desire antisense target and further antisense template will be designed according to Watson-Crick model. This article explained all information about how our new approach is best for designing antisense template against SARS-CoV-2 and many lethal infectious viruses etc.

bioinformatics↗

bioRxiv2020

Plasmids encode niche-specific traits in Lactobacillaceae

The species of family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbor plasmids that encode important genes. In this study, we performed comparative genomic analysis of the publically available data of 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-third of the species had at least one plasmid-harboring strain. Plasmid abundance and GC content were significantly lower in the vertebrate-adapted species as compared to the nomadic and free-living species. Hierarchical clustering (HCL) highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-adapted species. EggNOG assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin-antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters, and major facilitator superfamily were found to be overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures are correlated to the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of the vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to the respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria. Impact statementThe bacteria of the family Lactobacillaceae are present in the wide range of habitats and play an important role in human health, fermented foods and chemical industries. A few studies have demonstrated the presence of plasmids in the individual strains of Lactobacillaceae species encoding various traits. Extensive data of genome sequences of the lactobacilli are becoming available; however, no comprehensive analysis of the plasmid-encoded genes and determining their biological relevance across lactobacilli has been undertaken at a larger scale. In this study, we explored the genomic content of 512 plasmids of Lactobacillaceae species and correlated it to the three types of these species according to their ecological niches - vertebrate-adapted, free-living and nomadic. Comparatively lower plasmid abundance and GC content in the vertebrate-adapted species could be correlated to the presence of these species in the nutrient-rich environment. The genomic content of the plasmids was consistent with the respective lifestyle adopted by lactobacilli suggesting that the plasmids might enhance the niche-specific fitness of the strains. The plethora of important genes present on the plasmids can also make them a highly useful tool in improving the probiotic, technological and food-related properties of lactobacilli. Data summaryNucleotide sequences of plasmids of Lactobacillus strains for which complete genome sequences were available were retrieved from the NCBI genome [https://www.ncbi.nlm.nih.gov/genome] and PATRIC 3.5.41 databases on 31st March 2019. The dataset includes 512 nucleotide sequences of plasmids of 282 strains belonging to genus Lactobacillus before its reclassification into several genera (1). Details of the plasmids have been given in Table S1.

genomics↗